Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	T	W	T	Q	M	Y	M	P	M	G	G	L	G	L	S	A	L	V	A	L	I	P	I	I	F	F	F	V	A	L	A	V	L	R	L	K	G	H	V	A	G	A	I	T	L	I	L	S	I	L	I	A	I	F	A	F	K	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																												?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	I	D	M	A	F	A	A	A	G	Y	G	F	I	Y	G	L	W	P	I	A	W	I	I	V	A	A	V	F	L	Y	K	L	T	V	A	S	G	Q	F	D	I	I	R	S	S	V	I	S	I	T	D	D	Q	R	L	Q	V	L	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	G	F	S	F	G	A	L	L	E	G	A	A	G	F	G	A	P	V	A	I	T	G	A	L	L	V	G	L	G	F	K	P	L	Y	A	A	G	L	C	L	I	A	N	T	A	P	V	A	F	G	A	L	G	V	P	I	L	V	A
Secondary structure
SS confidence
Disorder																																																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	Q	V	T	G	I	D	P	F	H	I	G	A	M	A	G	R	Q	L	P	F	L	S	V	L	V	P	F	W	L	V	A	M	M	D	G	W	K	G	V	K	E	T	W	P	A	A	L	V	A	G	G	S	F	A	V	T	Q	F	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		T	S	N	Y	I	G	P	E	L	P	D	I	T	S	A	L	V	S	I	V	S	L	A	L	F	L	K	V	W	R	P	K	N	T	E	T	A	I	S	M	G	Q	S	A	G	A	M	V	V	N	K	P	S	S	G	G	P	V	P	S
Secondary structure
SS confidence
Disorder																																			?	?	?	?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		E	Y	S	L	G	Q	I	I	R	A	W	S	P	F	L	I	L	T	V	L	V	T	I	W	T	M	K	P	F	K	A	L	F	A	P	G	G	A	F	Y	S	L	V	I	N	F	Q	I	P	H	L	H	Q	Q	V	L	K	A	A	P
Secondary structure
SS confidence
Disorder		?	?	?																								?	?			?	?	?	?		?		?	?														?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		I	V	A	Q	P	T	P	M	D	A	V	F	K	F	D	P	L	S	A	G	G	T	A	I	F	I	A	A	I	I	S	I	F	I	L	G	V	G	I	K	K	G	I	G	V	F	A	E	T	L	I	S	L	K	W	P	I	L	S	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		G	M	V	L	A	F	A	F	V	T	N	Y	S	G	M	S	T	T	L	A	L	V	L	A	G	T	G	V	M	F	P	F	F	S	P	F	L	G	W	L	G	V	F	L	T	G	S	D	T	S	S	N	A	L	F	G	S	L	Q	S
Secondary structure
SS confidence
Disorder												?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence		T	T	A	Q	Q	I	N	V	S	D	T	L	L	V	A	A	N	T	S	G	G	V	T	G	K	M	I	S	P	Q	S	I	A	V	A	C	A	A	T	G	M	V	G	R	E	S	E	L	F	R	Y	T	V	K	H	S	L	I	F	A
Secondary structure
SS confidence
Disorder							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560
Sequence		S	V	I	G	I	I	T	L	L	Q	A	Y	V	F	T	G	M	L	V	S
Secondary structure
SS confidence
Disorder																?	?	?	?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 1z96 chain A domain 1 Region: 146 - 164 Aligned: 19 Modelled: 19 Confidence: 27.7% Identity: 53% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 1cuk chain A domain 1 Region: 146 - 156 Aligned: 11 Modelled: 11 Confidence: 21.4% Identity: 64% Fold: RuvA C-terminal domain-like Superfamily: DNA helicase RuvA subunit, C-terminal domain Family: DNA helicase RuvA subunit, C-terminal domain Phyre2 PDB 2axt chain K domain 1 Region: 10 - 39 Aligned: 30 Modelled: 30 Confidence: 18.3% Identity: 17% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein K, PsbK Family: PsbK-like Phyre2 PDB 2lbg chain A Region: 455 - 470 Aligned: 16 Modelled: 16 Confidence: 18.2% Identity: 38% PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles Phyre2 PDB 3a0b chain K Region: 10 - 39 Aligned: 30 Modelled: 30 Confidence: 10.8% Identity: 17% PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 1y60 chain A Region: 466 - 486 Aligned: 21 Modelled: 21 Confidence: 8.3% Identity: 19% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: Formaldehyde-activating enzyme, FAE Phyre2 PDB 3orc chain A Region: 479 - 500 Aligned: 22 Modelled: 22 Confidence: 8.2% Identity: 27% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 2z3x chain C Region: 477 - 507 Aligned: 31 Modelled: 31 Confidence: 8.1% Identity: 16% PDB header:dna binding protein/dna Chain: C: PDB Molecule:small, acid-soluble spore protein c; PDBTitle: structure of a protein-dna complex essential for dna2 protection in spore of bacillus species Phyre2 PDB 2knc chain A Region: 249 - 284 Aligned: 36 Modelled: 36 Confidence: 7.2% Identity: 14% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3a0h chain K Region: 10 - 39 Aligned: 30 Modelled: 30 Confidence: 7.2% Identity: 17% PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3a0b chain K Region: 10 - 39 Aligned: 30 Modelled: 30 Confidence: 6.8% Identity: 17% PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 1d1l chain A Region: 479 - 500 Aligned: 22 Modelled: 22 Confidence: 5.4% Identity: 27% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 2i7p chain A domain 1 Region: 455 - 468 Aligned: 14 Modelled: 14 Confidence: 5.4% Identity: 21% Fold: Ribonuclease H-like motif Superfamily: Actin-like ATPase domain Family: Fumble-like Phyre2 PDB 2o01 chain F Region: 447 - 461 Aligned: 15 Modelled: 15 Confidence: 5.3% Identity: 33% PDB header:photosynthesis Chain: F: PDB Molecule:photosystem i reaction center subunit iii, PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 PDB 2pij chain B Region: 479 - 500 Aligned: 22 Modelled: 22 Confidence: 5.3% Identity: 23% PDB header:transcription Chain: B: PDB Molecule:prophage pfl 6 cro; PDBTitle: structure of the cro protein from prophage pfl 6 in pseudomonas2 fluorescens pf-5 Phyre2 PDB 1jb0 chain F Region: 447 - 461 Aligned: 15 Modelled: 15 Confidence: 5.2% Identity: 33% Fold: Single transmembrane helix Superfamily: Subunit III of photosystem I reaction centre, PsaF Family: Subunit III of photosystem I reaction centre, PsaF Phyre2 PDB 2nww chain A domain 1 Region: 522 - 555 Aligned: 34 Modelled: 34 Confidence: 5.2% Identity: 15% Fold: Proton glutamate symport protein Superfamily: Proton glutamate symport protein Family: Proton glutamate symport protein Phyre2 1 d1z96a1 2 d1cuka1 3 d2axtk1 4 c2lbgA_ 5 c3a0bK_ 6 d1y60a_ 7 d3orca_ 8 c2z3xC_ 9 c2kncA_ 10 c3a0hk_ 11 c3a0bk_ 12 d1d1la_ 13 d2i7pa1 14 c2o01F_ 15 c2pijB_ 16 d1jb0f_ 17 d2nwwa1

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 d1z96a1 27.7 53 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 2 d1cuka1 21.4 64 Fold:RuvA C-terminal domain-like Superfamily:DNA helicase RuvA subunit, C-terminal domain Family:DNA helicase RuvA subunit, C-terminal domain 3 d2axtk1 18.3 17 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein K, PsbK Family:PsbK-like 4 c2lbgA_ 18.2 38 PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles 5 c3a0bK_ 10.8 17 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex 6 d1y60a_ 8.3 19 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Formaldehyde-activating enzyme, FAE 7 d3orca_ 8.2 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 8 c2z3xC_ 8.1 16 PDB header:dna binding protein/dna Chain: C: PDB Molecule:small, acid-soluble spore protein c; PDBTitle: structure of a protein-dna complex essential for dna2 protection in spore of bacillus species 9 c2kncA_ 7.2 14 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 10 c3a0hk_ 7.2 17 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of i-substituted photosystem ii complex 11 c3a0bk_ 6.8 17 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex 12 d1d1la_ 5.4 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 13 d2i7pa1 5.4 21 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Fumble-like 14 c2o01F_ 5.3 33 PDB header:photosynthesis Chain: F: PDB Molecule:photosystem i reaction center subunit iii, PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 15 c2pijB_ 5.3 23 PDB header:transcription Chain: B: PDB Molecule:prophage pfl 6 cro; PDBTitle: structure of the cro protein from prophage pfl 6 in pseudomonas2 fluorescens pf-5 16 d1jb0f_ 5.2 33 Fold:Single transmembrane helix Superfamily:Subunit III of photosystem I reaction centre, PsaF Family:Subunit III of photosystem I reaction centre, PsaF 17 d2nwwa1 5.2 15 Fold:Proton glutamate symport protein Superfamily:Proton glutamate symport protein Family:Proton glutamate symport protein

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0